Reports of Rooney being sold became viral after Ferguson dropped Rooney to the bench for Tuesday's Champions League second leg tie against Real Madrid.
"He will be here next year, you have my word on that," Ferguson said. "There's absolutely no issue between Wayne Rooney and me, there is absolutely no problem," he said.
Ferguson was too 'distraught' to talk after the defeat to Real with referee Cuneyt Cakir wrongly sending off Nani for a challenge on Alvaro Arbeloa. But Ferguson continued to talk about reports suggesting that Rooney would be sold in the summer.
Rooney is one of the highest earners at United with £250,000-a-week in wages and had been linked with a move to a number of clubs, including PSG and Manchester City.
"To suggest we don't talk on the training ground is absolute nonsense," Ferguson said.
"Wayne understood the reasons for not playing him were completely tactical and I think we were right. He understood exactly what we were doing. I explained it to him before we announced the team and he was fine. You don't always get it right but I think we got it right," he said.
Rooney has scored 14 goals this season from 24 starts and has been playing in a deeper role to accomadate Robin van Persie.
On the decision of sending off Nani by referee Cakir Ferguson said, "It is hard to keep your faith when you have things like that."
"But in the cold light of day, we have to get on with it. Nothing can be done. This is another day in the history of our club - not a good day, but a day," he said.